Merge pull request #551 from saalfeldlab/feat/1.6.0

Feat/1.6.0

README.md

@@ -24,7 +24,9 @@ Paintera is a general visualization tool for 3D volumetric data and proof-readin
 
 ## Installation
 
-The current version release version can be installed from the [Github Releases](https://github.com/saalfeldlab/paintera/releases)
+The latest release can be installed from the [Github Releases](https://github.com/saalfeldlab/paintera/releases)
+
+[![GitHub Release](https://img.shields.io/github/v/release/saalfeldlab/paintera)](https://github.com/saalfeldlab/paintera/releases)
 
 
 

pom.xml

@@ -10,7 +10,7 @@
 
 	<groupId>org.janelia.saalfeldlab</groupId>
 	<artifactId>paintera</artifactId>
-	<version>1.5.2-SNAPSHOT</version>
+	<version>1.6.0-SNAPSHOT</version>
 
 	<name>Paintera</name>
 	<description>New Era Painting and annotation tool</description>
@@ -58,7 +58,7 @@
 
 		<!-- JavaFx Version-->
 		<javafx.version>22.0.1</javafx.version>
-		<saalfx.version>2.1.0</saalfx.version>
+		<saalfx.version>2.2.0</saalfx.version>
 		<testfx.version>4.0.16-alpha</testfx.version>
 
 		<alphanumeric-comparator.version>1.4.1</alphanumeric-comparator.version>
@@ -68,7 +68,7 @@
 		<main-class>org.janelia.saalfeldlab.paintera.Paintera</main-class>
 		<app.name>Paintera</app.name>
 		<app.package>paintera</app.package>
-		<app.version>1.5.1</app.version>
+		<app.version>1.6.0</app.version>
 
 		<jvm.modules>javafx.base,javafx.controls,javafx.fxml,javafx.media,javafx.swing,javafx.web,javafx.graphics,java.naming,java.management,java.sql</jvm.modules>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

src/main/java/org/janelia/saalfeldlab/paintera/control/OrthogonalViewsValueDisplayListener.java

@@ -49,7 +49,9 @@ public OrthogonalViewsValueDisplayListener(
 
 	public void addHandlers(ViewerPanelFX viewer) {
 
-		listeners.putIfAbsent(viewer, new ValueDisplayListener<>(viewer, currentSource, interpolation, submitValue));
+		if (!listeners.containsKey(viewer)) {
+			listeners.put(viewer, new ValueDisplayListener<>(viewer, currentSource, interpolation, submitValue));
+		}
 
 		viewer.getDisplay().addEventFilter(MouseEvent.MOUSE_MOVED, listeners.get(viewer));
 		viewer.addTransformListener(listeners.get(viewer));

src/main/java/org/janelia/saalfeldlab/paintera/control/actions/AllowedActions.java

@@ -58,7 +58,7 @@ public final class AllowedActions {
 	@Nonnull
 	public static final AllowedActions VIEW_LABELS = new AllowedActionsBuilder()
 			.add(NAVIGATION)
-			.add(LabelActionType.Toggle, LabelActionType.Append, LabelActionType.SelectAll)
+			.add(LabelActionType.readOnly())
 			.create();
 
 	private final Set<ActionType> actions;

src/main/java/org/janelia/saalfeldlab/paintera/control/actions/LabelActionType.java

@@ -3,13 +3,29 @@
 import java.util.EnumSet;
 
 public enum LabelActionType implements ActionType {
-	Toggle,
+	Toggle(true),
 	Append,
 	CreateNew,
-	Lock,
+	Lock(true),
 	Merge,
 	Split,
-	SelectAll;
+	SelectAll(true);
+
+	//TODO Caleb: consider moving this to ActionType. Maybe others too
+	private final boolean readOnly;
+
+	LabelActionType() {
+		this(false);
+	}
+
+	LabelActionType(boolean readOnly) {
+		this.readOnly = readOnly;
+	}
+
+	public boolean isReadOnly() {
+
+		return readOnly;
+	}
 
 	public static EnumSet<LabelActionType> of(final LabelActionType first, final LabelActionType... rest) {
 
@@ -21,6 +37,13 @@ public static EnumSet<LabelActionType> all() {
 		return EnumSet.allOf(LabelActionType.class);
 	}
 
+	public static EnumSet<LabelActionType> readOnly() {
+
+		var readOnly = EnumSet.noneOf(LabelActionType.class);
+		all().stream().filter(LabelActionType::isReadOnly).forEach(readOnly::add);
+		return readOnly;
+	}
+
 	public static EnumSet<LabelActionType> none() {
 
 		return EnumSet.noneOf(LabelActionType.class);

src/main/java/org/janelia/saalfeldlab/paintera/control/actions/MenuActionType.java

@@ -6,8 +6,15 @@
 public enum MenuActionType implements ActionType {
 	AddSource,
 	ChangeActiveSource,
-	SidePanel,
+	ToggleSidePanel,
+	ResizePanel,
+	ToggleToolBarVisibility,
+	ToggleMenuBarVisibility,
+	ToggleMenuBarMode,
+	ToggleStatusBarVisibility,
+	ToggleStatusBarMode,
 	ToggleMaximizeViewer,
+	ResizeViewers,
 	OrthoslicesContextMenu,
 	SaveProject,
 	CommitCanvas,

src/main/java/org/janelia/saalfeldlab/paintera/control/actions/PaintActionType.java

@@ -11,7 +11,8 @@ public enum PaintActionType implements ActionType {
 	SetBrushSize,
 	SetBrushDepth,
 	ShapeInterpolation,
-	SegmentAnything;
+	SegmentAnything,
+	Smooth;
 
 	public static EnumSet<PaintActionType> of(final PaintActionType first, final PaintActionType... rest) {
 

src/main/java/org/janelia/saalfeldlab/paintera/control/navigation/ValueDisplayListener.java

@@ -14,12 +14,10 @@
 import net.imglib2.Volatile;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.realtransform.RealViews;
-import net.imglib2.type.label.VolatileLabelMultisetType;
 import net.imglib2.view.composite.Composite;
 import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerPanelFX;
 import org.janelia.saalfeldlab.fx.Tasks;
 import org.janelia.saalfeldlab.paintera.data.ChannelDataSource;
-import org.janelia.saalfeldlab.paintera.data.DataSource;
 
 import java.util.Arrays;
 import java.util.HashMap;
@@ -67,7 +65,7 @@ public ValueDisplayListener(
 							),
 							affine
 					).realRandomAccess();
-				}, currentSource, viewer.getRenderUnit().getScreenScalesProperty(), viewerTransformChanged
+				}, currentSource, viewer.getRenderUnit().getScreenScalesProperty(), viewerTransformChanged, viewer.getRenderUnit().getRepaintRequestProperty()
 		);
 
 		this.accessBinding.addListener((obs, old, newAccess) -> {

src/main/java/org/janelia/saalfeldlab/paintera/id/IdService.java

@@ -108,7 +108,7 @@ static long randomTemporaryId() {
 
 	static boolean isTemporary(final long id) {
 
-		return id > FIRST_TEMPORARY_ID && id < LAST_TEMPORARY_ID;
+		return id >= FIRST_TEMPORARY_ID && id < LAST_TEMPORARY_ID;
 	}
 
 	class IdServiceNotProvided implements IdService {

src/main/java/org/janelia/saalfeldlab/paintera/id/LocalIdService.java

@@ -1,5 +1,6 @@
 package org.janelia.saalfeldlab.paintera.id;
 
+import java.util.Arrays;
 import java.util.stream.LongStream;
 
 public class LocalIdService implements IdService {
@@ -19,15 +20,13 @@ public LocalIdService(final long next) {
 
 	@Override public long nextTemporary() {
 
-		final var temp = nextTemp;
-		nextTemp += 1;
-		return temp;
+		return IdService.randomTemps.next();
 	}
 
 	@Override public long[] nextTemporary(int n) {
 
-		final long[] tempIds = LongStream.range(nextTemp, nextTemp + n).toArray();
-		nextTemp += n;
+		final long[] tempIds = new long[n];
+		Arrays.setAll(tempIds, it -> IdService.randomTemps.next());
 		return tempIds;
 	}
 

src/main/java/org/janelia/saalfeldlab/paintera/stream/HighlightingStreamConverter.java

@@ -27,8 +27,8 @@
 import java.util.Map;
 
 public abstract class HighlightingStreamConverter<T>
-		implements Converter<T, ARGBType>, SeedProperty, WithAlpha, ColorFromSegmentId, HideLockedSegments,
-		UserSpecifiedColors {
+		implements Converter<T, ARGBType>,
+		SeedProperty, WithAlpha, ColorFromSegmentId, HideLockedSegments, UserSpecifiedColors {
 
 	private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 
@@ -132,7 +132,10 @@ public static <T> HighlightingStreamConverter<T> forType(
 			return (HighlightingStreamConverter<T>)new HighlightingStreamConverterLabelMultisetType(stream);
 		}
 		if (t instanceof Volatile<?> && ((Volatile<?>)t).get() instanceof IntegerType<?>) {
-			return (HighlightingStreamConverter<T>)new HighlightingStreamConverterIntegerType(stream);
+			return (HighlightingStreamConverter<T>)new HighlightingStreamConverterVolatileIntegerType<>(stream);
+		}
+		if (t instanceof IntegerType<?>) {
+			return (HighlightingStreamConverter<T>)new HighlightingStreamConverterIntegerType<>(stream);
 		}
 
 		return null;

src/main/java/org/janelia/saalfeldlab/paintera/stream/HighlightingStreamConverterIntegerType.java

@@ -8,7 +8,7 @@
 
 import java.lang.invoke.MethodHandles;
 
-public class HighlightingStreamConverterIntegerType<I extends IntegerType<I>, V extends Volatile<I>> extends HighlightingStreamConverter<V> {
+public class HighlightingStreamConverterIntegerType<I extends IntegerType<I>> extends HighlightingStreamConverter<I> {
 
 	private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
 
@@ -19,9 +19,9 @@ public HighlightingStreamConverterIntegerType(final AbstractHighlightingARGBStre
 	}
 
 	@Override
-	public void convert(final V input, final ARGBType output) {
+	public void convert(final I input, final ARGBType output) {
 
-		output.set(stream.argb(input.get().getIntegerLong()));
+		output.set(stream.argb(input.getIntegerLong()));
 	}
 
 }

src/main/java/org/janelia/saalfeldlab/paintera/stream/HighlightingStreamConverterVolatileIntegerType.java

@@ -0,0 +1,12 @@
+package org.janelia.saalfeldlab.paintera.stream;
+
+import net.imglib2.Volatile;
+import net.imglib2.type.numeric.IntegerType;
+
+public class HighlightingStreamConverterVolatileIntegerType<I extends IntegerType<I>, V extends Volatile<I>> extends HighlightingStreamConverterVolatileType<I, V> {
+
+	public HighlightingStreamConverterVolatileIntegerType(final AbstractHighlightingARGBStream stream) {
+
+		super(stream, new HighlightingStreamConverterIntegerType(stream));
+	}
+}

src/main/java/org/janelia/saalfeldlab/paintera/stream/HighlightingStreamConverterVolatileLabelMultisetType.java

@@ -1,28 +1,12 @@
 package org.janelia.saalfeldlab.paintera.stream;
 
+import net.imglib2.type.label.LabelMultisetType;
 import net.imglib2.type.label.VolatileLabelMultisetType;
-import net.imglib2.type.numeric.ARGBType;
 
-public class HighlightingStreamConverterVolatileLabelMultisetType extends HighlightingStreamConverter<VolatileLabelMultisetType> {
+public class HighlightingStreamConverterVolatileLabelMultisetType extends HighlightingStreamConverterVolatileType<LabelMultisetType, VolatileLabelMultisetType> {
 
-	private final HighlightingStreamConverterLabelMultisetType nonVolatileConverter;
 	public HighlightingStreamConverterVolatileLabelMultisetType(final AbstractHighlightingARGBStream stream) {
 
-		super(stream);
-		nonVolatileConverter = new HighlightingStreamConverterLabelMultisetType(stream);
-	}
-
-	public HighlightingStreamConverterLabelMultisetType getNonVolatileConverter() {
-		return nonVolatileConverter;
-	}
-
-	@Override
-	public void convert(final VolatileLabelMultisetType input, final ARGBType output) {
-
-		final boolean isValid = input.isValid();
-		if (!isValid) {
-			return;
-		}
-		nonVolatileConverter.convert(input.get(), output);
+		super(stream, new HighlightingStreamConverterLabelMultisetType(stream));
 	}
 }

src/main/java/org/janelia/saalfeldlab/paintera/stream/HighlightingStreamConverterVolatileType.java

@@ -0,0 +1,29 @@
+package org.janelia.saalfeldlab.paintera.stream;
+
+import net.imglib2.Volatile;
+import net.imglib2.type.numeric.ARGBType;
+
+public abstract class HighlightingStreamConverterVolatileType<I, V extends Volatile<I>> extends HighlightingStreamConverter<V> {
+
+	protected final HighlightingStreamConverter<I> nonVolatileConverter;
+
+	public HighlightingStreamConverterVolatileType(AbstractHighlightingARGBStream stream, HighlightingStreamConverter<I> nonVolatileConverter) {
+
+		super(stream);
+		this.nonVolatileConverter = nonVolatileConverter;
+	}
+
+	public HighlightingStreamConverter<I> getNonVolatileConverter() {
+
+		return nonVolatileConverter;
+	}
+
+	@Override public void convert(V input, ARGBType output) {
+
+		final boolean isValid = input.isValid();
+		if (!isValid) {
+			return;
+		}
+		getNonVolatileConverter().convert(input.get(), output);
+	}
+}

src/main/java/org/janelia/saalfeldlab/paintera/viewer3d/Scene3DHandler.java

@@ -64,7 +64,7 @@ public Scene3DHandler(final Viewer3DFX viewer) {
 		ActionSet.installActionSet(viewer, additionalCommands);
 
 		Paintera.whenPaintable(() -> {
-			/* These depend on the keyTracker in the PainteraMainWindow, so cannot be installed until the MainWindow is done intializing. */
+			/* These depend on the keyTracker in the PainteraMainWindow, so cannot be installed until the MainWindow is done initializing. */
 			final var zoomActionSet = zoom3D();
 			ActionSet.installActionSet(viewer, zoomActionSet);
 		});
@@ -187,16 +187,16 @@ private void drag(MouseEvent event) {
 
 	private class Rotate3DView extends DragActionSet {
 
-		private double baseSpeed = 1.0;
+		private double baseSpeed = 0.25;
 		private double factor = 1.0;
 
 		private double speed = baseSpeed * factor;
 
-		private final static double SLOW_FACTOR = 0.1;
+		private final static double SLOW_FACTOR = 0.5;
 
 		private final static double NORMAL_FACTOR = 1;
 
-		private final static double FAST_FACTOR = 2;
+		private final static double FAST_FACTOR = 2.0;
 
 		private final Affine affineDragStart = new Affine();
 

src/main/kotlin/org/janelia/saalfeldlab/bdv/fx/viewer/SourceUtils.kt

@@ -8,6 +8,7 @@ import net.imglib2.realtransform.AffineTransform3D
 import net.imglib2.type.numeric.ARGBType
 import org.janelia.saalfeldlab.paintera.data.DataSource
 import org.janelia.saalfeldlab.paintera.stream.HighlightingStreamConverterVolatileLabelMultisetType
+import org.janelia.saalfeldlab.paintera.stream.HighlightingStreamConverterVolatileType
 
 //FIXME Caleb: These are both private because imho this is a bit of a hack.
 // We want to Paintera's DataSource implemenet Source over the volatile type,
@@ -59,7 +60,7 @@ internal fun <D : Any> getDataSourceAndConverter(sourceAndConverter: SourceAndCo
 	val unwrappedDataSource = UnwrappedDataSource(data)
 
 	val converter = sourceAndConverter.converter.let {
-		(it as? HighlightingStreamConverterVolatileLabelMultisetType)?.nonVolatileConverter ?: it
+		(it as? HighlightingStreamConverterVolatileType<*, *>)?.nonVolatileConverter ?: it
 	} as Converter<D, ARGBType>
 
 	return WrappedSourceAndConverter(sourceAndConverter, unwrappedDataSource, converter)

src/main/kotlin/org/janelia/saalfeldlab/bdv/fx/viewer/render/ViewerRenderUnit.kt

@@ -5,6 +5,7 @@ import org.janelia.saalfeldlab.bdv.fx.viewer.ViewerState
 import bdv.viewer.Interpolation
 import bdv.viewer.Source
 import bdv.viewer.render.AccumulateProjectorFactory
+import javafx.beans.property.SimpleBooleanProperty
 import net.imglib2.parallel.TaskExecutor
 import net.imglib2.realtransform.AffineTransform3D
 import net.imglib2.type.numeric.ARGBType
@@ -32,10 +33,36 @@ open class ViewerRenderUnit(
 	renderingTaskExecutor,
 	useVolatileIfAvailable = true
 ) {
+
+	val repaintRequestProperty = SimpleBooleanProperty()
+
 	override fun paint() {
 		if (viewerStateSupplier.get()?.isVisible == true)
 			super.paint()
 	}
+
+	private fun notifyRepaintObservable() = repaintRequestProperty.set(!repaintRequestProperty.value)
+
+	override fun requestRepaint() {
+		super.requestRepaint()
+		notifyRepaintObservable()
+	}
+
+	override fun requestRepaint(screenScaleIndex: Int) {
+		super.requestRepaint(screenScaleIndex)
+		notifyRepaintObservable()
+	}
+
+	override fun requestRepaint(min: LongArray?, max: LongArray?) {
+		super.requestRepaint(min, max)
+		notifyRepaintObservable()
+	}
+
+	override fun requestRepaint(screenScaleIndex: Int, min: LongArray?, max: LongArray?) {
+		super.requestRepaint(screenScaleIndex, min, max)
+		notifyRepaintObservable()
+	}
+
 	companion object {
 
 		private fun Supplier<ViewerState?>.getRenderState() : () -> RenderUnitState? = {